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(-) Description

Title :  STRUCTURAL BASIS FOR THE RECOGNITION OF LYS48-LINKED POLYUBIQUITIN CHAIN BY THE JOSEPHIN DOMAIN OF ATAXIN-3, A PUTATIVE DEUBIQUITINATING ENZYME
 
Authors :  A. Sumiyoshi
Date :  03 May 06  (Deposition) - 22 May 07  (Release) - 31 Dec 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Deubiquitinating Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Satoh, A. Sumiyoshi, M. Yagi-Utsumi, E. Sakata, H. Sasakawa, E. Kurimoto, Y. Yamaguchi, W. Li, C. A. Joazeiro, T. Hirokawa, K. Kato
Mode Of Substrate Recognition By The Josephin Domain Of Ataxin-3, Which Has An Endo-Type Deubiquitinase Activity.
Febs Lett. V. 588 4422 2014
PubMed-ID: 25448680  |  Reference-DOI: 10.1016/J.FEBSLET.2014.10.013

(-) Compounds

Molecule 1 - ATAXIN-3
    ChainsA
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentJOSEPHIN DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMACHADO-JOSEPH DISEASE PROTEIN 1, SPINOCEREBELLAR ATAXIA TYPE 3 PROTEIN

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DOS)

(-) Sites  (0, 0)

(no "Site" information available for 2DOS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DOS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DOS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DOS)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JOSEPHINPS50957 Josephin domain profile.ATX3_HUMAN1-180  1A:1-171
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JOSEPHINPS50957 Josephin domain profile.ATX3_HUMAN1-180  1A:1-171

(-) Exons   (0, 0)

(no "Exon" information available for 2DOS)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:171
 aligned with ATX3_HUMAN | P54252 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
           ATX3_HUMAN     1 MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGDLPD 171
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh............hhhhhhhhhhh...eeee..hhhhhhhh.......eeeeee..eeeeeeee..eeeee.......eeehhhhhhhhhhhhhhhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE JOSEPHIN  PDB: A:1-171 UniProt: 1-180                                                                                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dos A   1 MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGDLPD 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2DOS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DOS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DOS)

(-) Gene Ontology  (46, 46)

NMR Structure(hide GO term definitions)
Chain A   (ATX3_HUMAN | P54252)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:1990380    Lys48-specific deubiquitinase activity    Hydrolysis of Lys48-linked ubiquitin unit(s) from a ubiquitinated protein.
    GO:0061578    Lys63-specific deubiquitinase activity    Hydrolysis of Lys63-Linked ubiquitin unit(s) from a ubiquitinated protein.
    GO:0001012    RNA polymerase II regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008242    omega peptidase activity    Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups).
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0034605    cellular response to heat    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0071218    cellular response to misfolded protein    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a misfolded protein stimulus.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0035640    exploration behavior    The specific behavior of an organism in response to a novel environment or stimulus.
    GO:0070932    histone H3 deacetylation    The modification of histone H3 by the removal of one or more acetyl groups.
    GO:0045104    intermediate filament cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising intermediate filaments and their associated proteins.
    GO:0000226    microtubule cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    GO:0006515    misfolded or incompletely synthesized protein catabolic process    The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.
    GO:0035520    monoubiquitinated protein deubiquitination    The removal of the ubiquitin group from a monoubiquitinated protein.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:1904294    positive regulation of ERAD pathway    Any process that activates or increases the frequency, rate or extent of ERAD pathway.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0071108    protein K48-linked deubiquitination    A protein deubiquitination process in which a K48-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is removed from a protein.
    GO:0070536    protein K63-linked deubiquitination    A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a protein.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:1904379    protein localization to cytosolic proteasome complex involved in ERAD pathway    Any protein localization to cytosolic proteasome complex that is involved in ERAD pathway. Following their retrotranslocation out of the endoplasmic reticulum, protein substrates must be shuttled to the cytosolic proteasome for degradation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0010810    regulation of cell-substrate adhesion    Any process that modulates the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0042405    nuclear inclusion body    An intranuclear focus at which aggregated proteins have been sequestered.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ATX3_HUMAN | P542521yzb 2aga 2jri 2klz 4wth 4ys9

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